From 64348594a5117099ff733e6b119eeb887139a49c Mon Sep 17 00:00:00 2001
From: Benney Au <benney_au@hotmail.com>
Date: Tue, 26 Nov 2024 12:08:22 +1100
Subject: [PATCH] fix incremental build

---
 Makefile            | 9 ++-------
 README.md           | 2 +-
 src/peprocessor.cpp | 2 +-
 3 files changed, 4 insertions(+), 9 deletions(-)

diff --git a/Makefile b/Makefile
index c066c86..7a4a7d4 100644
--- a/Makefile
+++ b/Makefile
@@ -28,7 +28,8 @@ ${BIN_TARGET}:${OBJ}
 static:${OBJ}
 	$(CXX) $(OBJ) -o ${BIN_TARGET} $(STATIC_LD_FLAGS)
 
-${DIR_OBJ}/%.o:${DIR_SRC}/%.cpp make_obj_dir
+${DIR_OBJ}/%.o:${DIR_SRC}/%.cpp
+	@mkdir -p $(@D)
 	$(CXX) -c $< -o $@ $(CXXFLAGS)
 
 .PHONY:clean
@@ -43,12 +44,6 @@ clean:
 		rm $(TARGET) ; \
 	fi
 
-make_obj_dir:
-	@if test ! -d $(DIR_OBJ) ; \
-	then \
-		mkdir $(DIR_OBJ) ; \
-	fi
-
 install:
 	install $(TARGET) $(BINDIR)/$(TARGET)
 	@echo "Installed."
diff --git a/README.md b/README.md
index 154e867..1378f46 100644
--- a/README.md
+++ b/README.md
@@ -357,7 +357,7 @@ means that 150bp are from read1, and 15bp are from read2. `fastp` prefers the ba
 Same as the [base correction feature](#base-correction-for-pe-data), this function is also based on overlapping detection, which has adjustable parameters `overlap_len_require (default 30)`, `overlap_diff_limit (default 5)` and `overlap_diff_percent_limit (default 20%)`. Please note that the reads should meet these three conditions simultaneously.
 
 # duplication rate and deduplication
-For both SE and PE data, fastp supports evaluating its duplication rate and removing duplicated reads/pairs. fastp considers one read as duplicated only if its all base pairs are identical as another one. This meas if there is a sequencing error or an N base, the read will not be treated as duplicated.
+For both SE and PE data, fastp supports evaluating its duplication rate and removing duplicated reads/pairs. fastp considers one read as duplicated only if its all base pairs are identical as another one. This means if there is a sequencing error or an N base, the read will not be treated as duplicated.
 
 ## duplication rate evaluation
 By default, fastp evaluates duplication rate, and this module may use 1G memory and take 10% ~ 20% more running time. If you don't need the duplication rate information, you can set `--dont_eval_duplication` to disable the duplication evaluation. But please be noted that, if deduplication (`--dedup`) option is enabled, then `--dont_eval_duplication` option is ignored.
diff --git a/src/peprocessor.cpp b/src/peprocessor.cpp
index e8d85d6..7ee4191 100644
--- a/src/peprocessor.cpp
+++ b/src/peprocessor.cpp
@@ -360,7 +360,7 @@ void PairEndProcessor::recycleToPool2(int tid, Read* r) {
 bool PairEndProcessor::processPairEnd(ReadPack* leftPack, ReadPack* rightPack, ThreadConfig* config){
     if(leftPack->count != rightPack->count) {
         cerr << endl;
-        cerr << "WARNNIG: different read numbers of the " << mPackProcessedCounter << " pack" << endl;
+        cerr << "WARNING: different read numbers of the " << mPackProcessedCounter << " pack" << endl;
         cerr << "Read1 pack size: " << leftPack->count << endl;
         cerr << "Read2 pack size: " << rightPack->count << endl;
         cerr << endl;